datasnakes · grabear · May 3, 2017 · Apr 24, 2017 · Apr 24, 2017 · Apr 24, 2017
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,11 @@
+*.gbff
+/manager/data
+*.log
+*.gbk
+*.pyc
+*.db
+*.ffn.best
+shiny_dir_mana.txt
+/.Rproj*
+/.idea
+/.idea/**
diff --git a/.idea/Vallender-Labs-Scripts.iml b/.idea/Vallender-Labs-Scripts.iml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/Aqua.txt → Orthologs/Aqua.txt b/Aqua.txt → Orthologs/Aqua.txt
diff --git a/biosql/README.md → Orthologs/biosql/README.md b/biosql/README.md → Orthologs/biosql/README.md
diff --git a/biosql/biosql/.idea/biosql.iml → Orthologs/biosql/biosql/.idea/biosql.iml b/biosql/biosql/.idea/biosql.iml → Orthologs/biosql/biosql/.idea/biosql.iml
diff --git a/.idea/dbnavigator.xml → ...ologs/biosql/biosql/.idea/dbnavigator.xml b/.idea/dbnavigator.xml → ...ologs/biosql/biosql/.idea/dbnavigator.xml
diff --git a/biosql/biosql/.idea/markdown-navigator.xml → ...iosql/biosql/.idea/markdown-navigator.xml b/biosql/biosql/.idea/markdown-navigator.xml → ...iosql/biosql/.idea/markdown-navigator.xml
diff --git a/.../markdown-navigator/profiles_settings.xml → .../markdown-navigator/profiles_settings.xml b/.../markdown-navigator/profiles_settings.xml → .../markdown-navigator/profiles_settings.xml
diff --git a/biosql/biosql/.idea/misc.xml → Orthologs/biosql/biosql/.idea/misc.xml b/biosql/biosql/.idea/misc.xml → Orthologs/biosql/biosql/.idea/misc.xml
diff --git a/biosql/biosql/.idea/modules.xml → Orthologs/biosql/biosql/.idea/modules.xml b/biosql/biosql/.idea/modules.xml → Orthologs/biosql/biosql/.idea/modules.xml
diff --git a/biosql/biosql/.idea/vcs.xml → Orthologs/biosql/biosql/.idea/vcs.xml b/biosql/biosql/.idea/vcs.xml → Orthologs/biosql/biosql/.idea/vcs.xml
diff --git a/biosql/biosql/.idea/workspace.xml → Orthologs/biosql/biosql/.idea/workspace.xml b/biosql/biosql/.idea/workspace.xml → Orthologs/biosql/biosql/.idea/workspace.xml
diff --git a/biosql/biosql/Changes → Orthologs/biosql/biosql/Changes b/biosql/biosql/Changes → Orthologs/biosql/biosql/Changes
diff --git a/biosql/biosql/INSTALL → Orthologs/biosql/biosql/INSTALL b/biosql/biosql/INSTALL → Orthologs/biosql/biosql/INSTALL
diff --git a/biosql/biosql/LICENSE → Orthologs/biosql/biosql/LICENSE b/biosql/biosql/LICENSE → Orthologs/biosql/biosql/LICENSE
diff --git a/biosql/biosql/README → Orthologs/biosql/biosql/README b/biosql/biosql/README → Orthologs/biosql/biosql/README
diff --git a/biosql/biosql/doc/README → Orthologs/biosql/biosql/doc/README b/biosql/biosql/doc/README → Orthologs/biosql/biosql/doc/README
diff --git a/biosql/biosql/doc/biopython/cor6_6.gb → ...ogs/biosql/biosql/doc/biopython/cor6_6.gb b/biosql/biosql/doc/biopython/cor6_6.gb → ...ogs/biosql/biosql/doc/biopython/cor6_6.gb
diff --git a/...ql/doc/biopython/python_biosql_basic.html → ...ql/doc/biopython/python_biosql_basic.html b/...ql/doc/biopython/python_biosql_basic.html → ...ql/doc/biopython/python_biosql_basic.html
diff --git a/...sql/doc/biopython/python_biosql_basic.pdf → ...sql/doc/biopython/python_biosql_basic.pdf b/...sql/doc/biopython/python_biosql_basic.pdf → ...sql/doc/biopython/python_biosql_basic.pdf
diff --git a/...sql/doc/biopython/python_biosql_basic.tex → ...sql/doc/biopython/python_biosql_basic.tex b/...sql/doc/biopython/python_biosql_basic.tex → ...sql/doc/biopython/python_biosql_basic.tex
diff --git a/...sql/doc/biopython/python_biosql_basic.txt → ...sql/doc/biopython/python_biosql_basic.txt b/...sql/doc/biopython/python_biosql_basic.txt → ...sql/doc/biopython/python_biosql_basic.txt
diff --git a/biosql/biosql/doc/biosql-ERD.pdf → Orthologs/biosql/biosql/doc/biosql-ERD.pdf b/biosql/biosql/doc/biosql-ERD.pdf → Orthologs/biosql/biosql/doc/biosql-ERD.pdf
diff --git a/biosql/biosql/doc/biosql-phylodb.graffle → .../biosql/biosql/doc/biosql-phylodb.graffle b/biosql/biosql/doc/biosql-phylodb.graffle → .../biosql/biosql/doc/biosql-phylodb.graffle
diff --git a/biosql/biosql/doc/biosql-phylodb.pdf → ...logs/biosql/biosql/doc/biosql-phylodb.pdf b/biosql/biosql/doc/biosql-phylodb.pdf → ...logs/biosql/biosql/doc/biosql-phylodb.pdf
diff --git a/biosql/biosql/doc/biosql-phylodb.png → ...logs/biosql/biosql/doc/biosql-phylodb.png b/biosql/biosql/doc/biosql-phylodb.png → ...logs/biosql/biosql/doc/biosql-phylodb.png
diff --git a/biosql/biosql/doc/biosql.html → Orthologs/biosql/biosql/doc/biosql.html b/biosql/biosql/doc/biosql.html → Orthologs/biosql/biosql/doc/biosql.html
diff --git a/...l/biosql/doc/bj_and_bsql_oracle_howto.htm → ...l/biosql/doc/bj_and_bsql_oracle_howto.htm b/...l/biosql/doc/bj_and_bsql_oracle_howto.htm → ...l/biosql/doc/bj_and_bsql_oracle_howto.htm
diff --git a/biosql/biosql/doc/logo/BioSQL-t.png → ...ologs/biosql/biosql/doc/logo/BioSQL-t.png b/biosql/biosql/doc/logo/BioSQL-t.png → ...ologs/biosql/biosql/doc/logo/BioSQL-t.png
diff --git a/biosql/biosql/doc/logo/BioSQL.graffle → ...ogs/biosql/biosql/doc/logo/BioSQL.graffle b/biosql/biosql/doc/logo/BioSQL.graffle → ...ogs/biosql/biosql/doc/logo/BioSQL.graffle
diff --git a/biosql/biosql/doc/logo/BioSQL.png → Orthologs/biosql/biosql/doc/logo/BioSQL.png b/biosql/biosql/doc/logo/BioSQL.png → Orthologs/biosql/biosql/doc/logo/BioSQL.png
diff --git a/biosql/biosql/doc/phylo-topo.graffle → ...logs/biosql/biosql/doc/phylo-topo.graffle b/biosql/biosql/doc/phylo-topo.graffle → ...logs/biosql/biosql/doc/phylo-topo.graffle
diff --git a/biosql/biosql/doc/phyloanalysis.graffle → ...s/biosql/biosql/doc/phyloanalysis.graffle b/biosql/biosql/doc/phyloanalysis.graffle → ...s/biosql/biosql/doc/phyloanalysis.graffle
diff --git a/biosql/biosql/doc/phyloanalysis.png → ...ologs/biosql/biosql/doc/phyloanalysis.png b/biosql/biosql/doc/phyloanalysis.png → ...ologs/biosql/biosql/doc/phyloanalysis.png
diff --git a/biosql/biosql/doc/schema-overview.txt → ...ogs/biosql/biosql/doc/schema-overview.txt b/biosql/biosql/doc/schema-overview.txt → ...ogs/biosql/biosql/doc/schema-overview.txt
diff --git a/biosql/biosql/doc/transitionmodel.graffle → ...biosql/biosql/doc/transitionmodel.graffle b/biosql/biosql/doc/transitionmodel.graffle → ...biosql/biosql/doc/transitionmodel.graffle
diff --git a/biosql/biosql/doc/transitionmodel.png → ...ogs/biosql/biosql/doc/transitionmodel.png b/biosql/biosql/doc/transitionmodel.png → ...ogs/biosql/biosql/doc/transitionmodel.png
diff --git a/biosql/biosql/scripts/load_itis_taxonomy.pl → ...osql/biosql/scripts/load_itis_taxonomy.pl b/biosql/biosql/scripts/load_itis_taxonomy.pl → ...osql/biosql/scripts/load_itis_taxonomy.pl
diff --git a/biosql/biosql/scripts/load_ncbi_taxonomy.pl → ...osql/biosql/scripts/load_ncbi_taxonomy.pl b/biosql/biosql/scripts/load_ncbi_taxonomy.pl → ...osql/biosql/scripts/load_ncbi_taxonomy.pl
diff --git a/biosql/biosql/scripts/parseTreesPG.pl → ...ogs/biosql/biosql/scripts/parseTreesPG.pl b/biosql/biosql/scripts/parseTreesPG.pl → ...ogs/biosql/biosql/scripts/parseTreesPG.pl
diff --git a/biosql/biosql/scripts/phyexport.pl → Orthologs/biosql/biosql/scripts/phyexport.pl b/biosql/biosql/scripts/phyexport.pl → Orthologs/biosql/biosql/scripts/phyexport.pl
diff --git a/biosql/biosql/scripts/phyimport.pl → Orthologs/biosql/biosql/scripts/phyimport.pl b/biosql/biosql/scripts/phyimport.pl → Orthologs/biosql/biosql/scripts/phyimport.pl
diff --git a/biosql/biosql/scripts/phyinit.pl → Orthologs/biosql/biosql/scripts/phyinit.pl b/biosql/biosql/scripts/phyinit.pl → Orthologs/biosql/biosql/scripts/phyinit.pl
diff --git a/biosql/biosql/scripts/phymod.pl → Orthologs/biosql/biosql/scripts/phymod.pl b/biosql/biosql/scripts/phymod.pl → Orthologs/biosql/biosql/scripts/phymod.pl
diff --git a/biosql/biosql/scripts/phyopt.pl → Orthologs/biosql/biosql/scripts/phyopt.pl b/biosql/biosql/scripts/phyopt.pl → Orthologs/biosql/biosql/scripts/phyopt.pl
diff --git a/biosql/biosql/scripts/phyreport.pl → Orthologs/biosql/biosql/scripts/phyreport.pl b/biosql/biosql/scripts/phyreport.pl → Orthologs/biosql/biosql/scripts/phyreport.pl
diff --git a/biosql/biosql/scripts/print-trees.pl → ...logs/biosql/biosql/scripts/print-trees.pl b/biosql/biosql/scripts/print-trees.pl → ...logs/biosql/biosql/scripts/print-trees.pl
diff --git a/biosql/biosql/scripts/tree-precompute.pl → .../biosql/biosql/scripts/tree-precompute.pl b/biosql/biosql/scripts/tree-precompute.pl → .../biosql/biosql/scripts/tree-precompute.pl
diff --git a/biosql/biosql/sql/biosql-phylodata-pg.sql → ...biosql/biosql/sql/biosql-phylodata-pg.sql b/biosql/biosql/sql/biosql-phylodata-pg.sql → ...biosql/biosql/sql/biosql-phylodata-pg.sql
diff --git a/biosql/biosql/sql/biosql-phylodb-mysql.sql → ...iosql/biosql/sql/biosql-phylodb-mysql.sql b/biosql/biosql/sql/biosql-phylodb-mysql.sql → ...iosql/biosql/sql/biosql-phylodb-mysql.sql
diff --git a/biosql/biosql/sql/biosql-phylodb-pg.sql → ...s/biosql/biosql/sql/biosql-phylodb-pg.sql b/biosql/biosql/sql/biosql-phylodb-pg.sql → ...s/biosql/biosql/sql/biosql-phylodb-pg.sql
diff --git a/biosql/biosql/sql/biosqldb-derby.sql → ...logs/biosql/biosql/sql/biosqldb-derby.sql b/biosql/biosql/sql/biosqldb-derby.sql → ...logs/biosql/biosql/sql/biosqldb-derby.sql
diff --git a/biosql/biosql/sql/biosqldb-hsqldb.sql → ...ogs/biosql/biosql/sql/biosqldb-hsqldb.sql b/biosql/biosql/sql/biosqldb-hsqldb.sql → ...ogs/biosql/biosql/sql/biosqldb-hsqldb.sql
diff --git a/biosql/biosql/sql/biosqldb-mysql.sql → ...logs/biosql/biosql/sql/biosqldb-mysql.sql b/biosql/biosql/sql/biosqldb-mysql.sql → ...logs/biosql/biosql/sql/biosqldb-mysql.sql
diff --git a/biosql/biosql/sql/biosqldb-ora/BS-DDL.sql → ...biosql/biosql/sql/biosqldb-ora/BS-DDL.sql b/biosql/biosql/sql/biosqldb-ora/BS-DDL.sql → ...biosql/biosql/sql/biosqldb-ora/BS-DDL.sql
diff --git a/...l/biosqldb-ora/BS-create-API-triggers.sql → ...l/biosqldb-ora/BS-create-API-triggers.sql b/...l/biosqldb-ora/BS-create-API-triggers.sql → ...l/biosqldb-ora/BS-create-API-triggers.sql
diff --git a/...biosql/sql/biosqldb-ora/BS-create-API.sql → ...biosql/sql/biosqldb-ora/BS-create-API.sql b/...biosql/sql/biosqldb-ora/BS-create-API.sql → ...biosql/sql/biosqldb-ora/BS-create-API.sql
diff --git a/...sql/biosqldb-ora/BS-create-Biosql-API.sql → ...sql/biosqldb-ora/BS-create-Biosql-API.sql b/...sql/biosqldb-ora/BS-create-Biosql-API.sql → ...sql/biosqldb-ora/BS-create-Biosql-API.sql
diff --git a/...ql/biosqldb-ora/BS-create-Biosql-API2.sql → ...ql/biosqldb-ora/BS-create-Biosql-API2.sql b/...ql/biosqldb-ora/BS-create-Biosql-API2.sql → ...ql/biosqldb-ora/BS-create-Biosql-API2.sql
diff --git a/...iosqldb-ora/BS-create-Biosql-usersyns.sql → ...iosqldb-ora/BS-create-Biosql-usersyns.sql b/...iosqldb-ora/BS-create-Biosql-usersyns.sql → ...iosqldb-ora/BS-create-Biosql-usersyns.sql
diff --git a/...biosql/sql/biosqldb-ora/BS-create-all.sql → ...biosql/sql/biosqldb-ora/BS-create-all.sql b/...biosql/sql/biosqldb-ora/BS-create-all.sql → ...biosql/sql/biosqldb-ora/BS-create-all.sql
diff --git a/...ql/biosqldb-ora/BS-create-ctx-indexes.sql → ...ql/biosqldb-ora/BS-create-ctx-indexes.sql b/...ql/biosqldb-ora/BS-create-ctx-indexes.sql → ...ql/biosqldb-ora/BS-create-ctx-indexes.sql
diff --git a/.../sql/biosqldb-ora/BS-create-ctx-prefs.sql → .../sql/biosqldb-ora/BS-create-ctx-prefs.sql b/.../sql/biosqldb-ora/BS-create-ctx-prefs.sql → .../sql/biosqldb-ora/BS-create-ctx-prefs.sql
diff --git a/...l/sql/biosqldb-ora/BS-create-ctx-proc.sql → ...l/sql/biosqldb-ora/BS-create-ctx-proc.sql b/...l/sql/biosqldb-ora/BS-create-ctx-proc.sql → ...l/sql/biosqldb-ora/BS-create-ctx-proc.sql
diff --git a/.../sql/biosqldb-ora/BS-create-ctx-wproc.sql → .../sql/biosqldb-ora/BS-create-ctx-wproc.sql b/.../sql/biosqldb-ora/BS-create-ctx-wproc.sql → .../sql/biosqldb-ora/BS-create-ctx-wproc.sql
diff --git a/...biosql/sql/biosqldb-ora/BS-create-ctx.sql → ...biosql/sql/biosqldb-ora/BS-create-ctx.sql b/...biosql/sql/biosqldb-ora/BS-create-ctx.sql → ...biosql/sql/biosqldb-ora/BS-create-ctx.sql
diff --git a/...l/sql/biosqldb-ora/BS-create-load-API.sql → ...l/sql/biosqldb-ora/BS-create-load-API.sql b/...l/sql/biosqldb-ora/BS-create-load-API.sql → ...l/sql/biosqldb-ora/BS-create-load-API.sql
diff --git a/...sql/sql/biosqldb-ora/BS-create-mviews.sql → ...sql/sql/biosqldb-ora/BS-create-mviews.sql b/...sql/sql/biosqldb-ora/BS-create-mviews.sql → ...sql/sql/biosqldb-ora/BS-create-mviews.sql
diff --git a/...biosql/sql/biosqldb-ora/BS-create-pkg.sql → ...biosql/sql/biosqldb-ora/BS-create-pkg.sql b/...biosql/sql/biosqldb-ora/BS-create-pkg.sql → ...biosql/sql/biosqldb-ora/BS-create-pkg.sql
diff --git a/...osql/sql/biosqldb-ora/BS-create-roles.sql → ...osql/sql/biosqldb-ora/BS-create-roles.sql b/...osql/sql/biosqldb-ora/BS-create-roles.sql → ...osql/sql/biosqldb-ora/BS-create-roles.sql
diff --git a/...ql/biosqldb-ora/BS-create-schema-user.sql → ...ql/biosqldb-ora/BS-create-schema-user.sql b/...ql/biosqldb-ora/BS-create-schema-user.sql → ...ql/biosqldb-ora/BS-create-schema-user.sql
diff --git a/...l/sql/biosqldb-ora/BS-create-synonyms.sql → ...l/sql/biosqldb-ora/BS-create-synonyms.sql b/...l/sql/biosqldb-ora/BS-create-synonyms.sql → ...l/sql/biosqldb-ora/BS-create-synonyms.sql
diff --git a/...ql/biosqldb-ora/BS-create-tablespaces.sql → ...ql/biosqldb-ora/BS-create-tablespaces.sql b/...ql/biosqldb-ora/BS-create-tablespaces.sql → ...ql/biosqldb-ora/BS-create-tablespaces.sql
diff --git a/...osql/sql/biosqldb-ora/BS-create-users.sql → ...osql/sql/biosqldb-ora/BS-create-users.sql b/...osql/sql/biosqldb-ora/BS-create-users.sql → ...osql/sql/biosqldb-ora/BS-create-users.sql
diff --git a/...osql/sql/biosqldb-ora/BS-create-views.sql → ...osql/sql/biosqldb-ora/BS-create-views.sql b/...osql/sql/biosqldb-ora/BS-create-views.sql → ...osql/sql/biosqldb-ora/BS-create-views.sql
diff --git a/.../sql/biosqldb-ora/BS-create-warehouse.sql → .../sql/biosqldb-ora/BS-create-warehouse.sql b/.../sql/biosqldb-ora/BS-create-warehouse.sql → .../sql/biosqldb-ora/BS-create-warehouse.sql
diff --git a/...l/sql/biosqldb-ora/BS-create-wh-views.sql → ...l/sql/biosqldb-ora/BS-create-wh-views.sql b/...l/sql/biosqldb-ora/BS-create-wh-views.sql → ...l/sql/biosqldb-ora/BS-create-wh-views.sql
diff --git a/...iosql/sql/biosqldb-ora/BS-ctx-rebuild.sql → ...iosql/sql/biosqldb-ora/BS-ctx-rebuild.sql b/...iosql/sql/biosqldb-ora/BS-ctx-rebuild.sql → ...iosql/sql/biosqldb-ora/BS-ctx-rebuild.sql
diff --git a/biosql/biosql/sql/biosqldb-ora/BS-defs.sql → ...iosql/biosql/sql/biosqldb-ora/BS-defs.sql b/biosql/biosql/sql/biosqldb-ora/BS-defs.sql → ...iosql/biosql/sql/biosqldb-ora/BS-defs.sql
diff --git a/biosql/biosql/sql/biosqldb-ora/BS-grants.sql → ...sql/biosql/sql/biosqldb-ora/BS-grants.sql b/biosql/biosql/sql/biosqldb-ora/BS-grants.sql → ...sql/biosql/sql/biosqldb-ora/BS-grants.sql
diff --git a/...ql/sql/biosqldb-ora/BS-prepopulate-db.sql → ...ql/sql/biosqldb-ora/BS-prepopulate-db.sql b/...ql/sql/biosqldb-ora/BS-prepopulate-db.sql → ...ql/sql/biosqldb-ora/BS-prepopulate-db.sql
diff --git a/...sql/biosqldb-ora/BS-refresh-warehouse.sql → ...sql/biosqldb-ora/BS-refresh-warehouse.sql b/...sql/biosqldb-ora/BS-refresh-warehouse.sql → ...sql/biosqldb-ora/BS-refresh-warehouse.sql
diff --git a/...ql/biosql/sql/biosqldb-ora/BS-zap-all.sql → ...ql/biosql/sql/biosqldb-ora/BS-zap-all.sql b/...ql/biosql/sql/biosqldb-ora/BS-zap-all.sql → ...ql/biosql/sql/biosqldb-ora/BS-zap-all.sql
diff --git a/biosql/biosql/sql/biosqldb-ora/INSTALL → ...gs/biosql/biosql/sql/biosqldb-ora/INSTALL b/biosql/biosql/sql/biosqldb-ora/INSTALL → ...gs/biosql/biosql/sql/biosqldb-ora/INSTALL
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkb b/.../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkb
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkg b/.../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/BSStd.pkg
diff --git a/...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkb → ...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkb b/...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkb → ...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkb
diff --git a/...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkg → ...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkg b/...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkg → ...l/sql/biosqldb-ora/PkgAPI/Biodatabase.pkg
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkb b/...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkb
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkg b/...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Bioentry.pkg
diff --git a/...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkb → ...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkb b/...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkb → ...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkb
diff --git a/...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkg → ...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkg b/...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkg → ...ql/biosqldb-ora/PkgAPI/Bioentry_Assoc.pkg
diff --git a/...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkb → ...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkb b/...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkb → ...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkb
diff --git a/...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkg → ...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkg b/...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkg → ...qldb-ora/PkgAPI/Bioentry_Dbxref_Assoc.pkg
diff --git a/...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkb → ...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkb b/...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkb → ...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkb
diff --git a/...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkg → ...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkg b/...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkg → ...sql/biosqldb-ora/PkgAPI/Bioentry_Path.pkg
diff --git a/...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkb → ...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkb b/...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkb → ...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkb
diff --git a/...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkg → ...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkg b/...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkg → ...b-ora/PkgAPI/Bioentry_Qualifier_Assoc.pkg
diff --git a/...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkb → ...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkb b/...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkb → ...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkb
diff --git a/...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkg → ...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkg b/...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkg → ...iosqldb-ora/PkgAPI/Bioentry_Ref_Assoc.pkg
diff --git a/...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkb → ...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkb b/...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkb → ...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkb
diff --git a/...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkg → ...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkg b/...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkg → ...iosqldb-ora/PkgAPI/Bioentry_Rel_Assoc.pkg
diff --git a/...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkb → ...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkb b/...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkb → ...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkb
diff --git a/...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkg → ...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkg b/...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkg → ...l/sql/biosqldb-ora/PkgAPI/Biosequence.pkg
diff --git a/...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkb → ...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkb b/...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkb → ...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkb
diff --git a/...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkg → ...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkg b/...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkg → ...sql/biosqldb-ora/PkgAPI/Chr_Map_Assoc.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkb b/...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkg b/...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Chromosome.pkg
diff --git a/...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkb → ...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkb b/...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkb → ...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkb
diff --git a/...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkg → ...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkg b/...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkg → ...iosql/sql/biosqldb-ora/PkgAPI/Comment.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkb → ...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkb b/...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkb → ...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkg → ...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkg b/...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkg → ...ql/sql/biosqldb-ora/PkgAPI/DB_Release.pkg
diff --git a/...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkb → ...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkb b/...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkb → ...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkb
diff --git a/...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkg → ...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkg b/...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkg → ...biosql/sql/biosqldb-ora/PkgAPI/Dbxref.pkg
diff --git a/...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkb → ...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkb b/...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkb → ...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkb
diff --git a/...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkg → ...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkg b/...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkg → ...ldb-ora/PkgAPI/Dbxref_Qualifier_Assoc.pkg
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Location.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Location.pkb b/...osql/sql/biosqldb-ora/PkgAPI/Location.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Location.pkb
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Location.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Location.pkg b/...osql/sql/biosqldb-ora/PkgAPI/Location.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Location.pkg
diff --git a/...b-ora/PkgAPI/Location_Qualifier_Assoc.pkb → ...b-ora/PkgAPI/Location_Qualifier_Assoc.pkb b/...b-ora/PkgAPI/Location_Qualifier_Assoc.pkb → ...b-ora/PkgAPI/Location_Qualifier_Assoc.pkb
diff --git a/...b-ora/PkgAPI/Location_Qualifier_Assoc.pkg → ...b-ora/PkgAPI/Location_Qualifier_Assoc.pkg b/...b-ora/PkgAPI/Location_Qualifier_Assoc.pkg → ...b-ora/PkgAPI/Location_Qualifier_Assoc.pkg
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkb b/...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkb → ...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkb
diff --git a/...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkg b/...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkg → ...osql/sql/biosqldb-ora/PkgAPI/Ontology.pkg
diff --git a/...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkb → ...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkb b/...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkb → ...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkb
diff --git a/...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkg → ...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkg b/...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkg → ...sql/biosqldb-ora/PkgAPI/Ontology_Term.pkg
diff --git a/...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkb → ...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkb b/...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkb → ...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkb
diff --git a/...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkg → ...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkg b/...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkg → ...osqldb-ora/PkgAPI/Ontology_Term_Assoc.pkg
diff --git a/...sql/sql/biosqldb-ora/PkgAPI/Reference.pkb → ...sql/sql/biosqldb-ora/PkgAPI/Reference.pkb b/...sql/sql/biosqldb-ora/PkgAPI/Reference.pkb → ...sql/sql/biosqldb-ora/PkgAPI/Reference.pkb
diff --git a/...sql/sql/biosqldb-ora/PkgAPI/Reference.pkg → ...sql/sql/biosqldb-ora/PkgAPI/Reference.pkg b/...sql/sql/biosqldb-ora/PkgAPI/Reference.pkg → ...sql/sql/biosqldb-ora/PkgAPI/Reference.pkg
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkb b/.../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkb
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkg b/.../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/SGAPI.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkb b/...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkg b/...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Seqfeature.pkg
diff --git a/.../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkb → .../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkb b/.../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkb → .../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkb
diff --git a/.../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkg → .../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkg b/.../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkg → .../biosqldb-ora/PkgAPI/Seqfeature_Assoc.pkg
diff --git a/...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkb → ...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkb b/...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkb → ...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkb
diff --git a/...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkg → ...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkg b/...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkg → ...db-ora/PkgAPI/Seqfeature_Dbxref_Assoc.pkg
diff --git a/...osqldb-ora/PkgAPI/Seqfeature_Location.pkb → ...osqldb-ora/PkgAPI/Seqfeature_Location.pkb b/...osqldb-ora/PkgAPI/Seqfeature_Location.pkb → ...osqldb-ora/PkgAPI/Seqfeature_Location.pkb
diff --git a/...osqldb-ora/PkgAPI/Seqfeature_Location.pkg → ...osqldb-ora/PkgAPI/Seqfeature_Location.pkg b/...osqldb-ora/PkgAPI/Seqfeature_Location.pkg → ...osqldb-ora/PkgAPI/Seqfeature_Location.pkg
diff --git a/...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkb → ...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkb b/...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkb → ...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkb
diff --git a/...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkg → ...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkg b/...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkg → ...l/biosqldb-ora/PkgAPI/Seqfeature_Path.pkg
diff --git a/...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkb → ...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkb b/...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkb → ...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkb
diff --git a/...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkg → ...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkg b/...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkg → ...ora/PkgAPI/Seqfeature_Qualifier_Assoc.pkg
diff --git a/...biosqldb-ora/PkgAPI/Seqfeature_Source.pkb → ...biosqldb-ora/PkgAPI/Seqfeature_Source.pkb b/...biosqldb-ora/PkgAPI/Seqfeature_Source.pkb → ...biosqldb-ora/PkgAPI/Seqfeature_Source.pkb
diff --git a/...biosqldb-ora/PkgAPI/Seqfeature_Source.pkg → ...biosqldb-ora/PkgAPI/Seqfeature_Source.pkg b/...biosqldb-ora/PkgAPI/Seqfeature_Source.pkg → ...biosqldb-ora/PkgAPI/Seqfeature_Source.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkb b/...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkg b/...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Similarity.pkg
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkb b/.../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkb → .../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkb
diff --git a/.../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkg b/.../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkg → .../biosql/sql/biosqldb-ora/PkgAPI/Taxon.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkb b/...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkg b/...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Taxon_Name.pkg
diff --git a/...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkb → ...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkb b/...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkb → ...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkb
diff --git a/...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkg → ...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkg b/...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkg → ...l/biosql/sql/biosqldb-ora/PkgAPI/Term.pkg
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkb b/...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkb → ...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkb
diff --git a/...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkg b/...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkg → ...ql/sql/biosqldb-ora/PkgAPI/Term_Assoc.pkg
diff --git a/...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkb → ...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkb b/...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkb → ...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkb
diff --git a/...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkg → ...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkg b/...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkg → ...biosqldb-ora/PkgAPI/Term_Dbxref_Assoc.pkg
diff --git a/...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkb → ...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkb b/...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkb → ...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkb
diff --git a/...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkg → ...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkg b/...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkg → ...sql/sql/biosqldb-ora/PkgAPI/Term_Path.pkg
diff --git a/.../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkb → .../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkb b/.../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkb → .../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkb
diff --git a/.../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkg → .../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkg b/.../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkg → .../sql/biosqldb-ora/PkgAPI/Term_Synonym.pkg
diff --git a/biosql/biosql/sql/biosqldb-ora/README → ...ogs/biosql/biosql/sql/biosqldb-ora/README b/biosql/biosql/sql/biosqldb-ora/README → ...ogs/biosql/biosql/sql/biosqldb-ora/README
diff --git a/...l/biosqldb-ora/load-trgs/Biodatabases.trg → ...l/biosqldb-ora/load-trgs/Biodatabases.trg b/...l/biosqldb-ora/load-trgs/Biodatabases.trg → ...l/biosqldb-ora/load-trgs/Biodatabases.trg
diff --git a/...sql/biosqldb-ora/load-trgs/Bioentries.trg → ...sql/biosqldb-ora/load-trgs/Bioentries.trg b/...sql/biosqldb-ora/load-trgs/Bioentries.trg → ...sql/biosqldb-ora/load-trgs/Bioentries.trg
diff --git a/...iosqldb-ora/load-trgs/Bioentry_Assocs.trg → ...iosqldb-ora/load-trgs/Bioentry_Assocs.trg b/...iosqldb-ora/load-trgs/Bioentry_Assocs.trg → ...iosqldb-ora/load-trgs/Bioentry_Assocs.trg
diff --git a/...a/load-trgs/Bioentry_Qualifier_Assocs.trg → ...a/load-trgs/Bioentry_Qualifier_Assocs.trg b/...a/load-trgs/Bioentry_Qualifier_Assocs.trg → ...a/load-trgs/Bioentry_Qualifier_Assocs.trg
diff --git a/...ldb-ora/load-trgs/Bioentry_Ref_Assocs.trg → ...ldb-ora/load-trgs/Bioentry_Ref_Assocs.trg b/...ldb-ora/load-trgs/Bioentry_Ref_Assocs.trg → ...ldb-ora/load-trgs/Bioentry_Ref_Assocs.trg
diff --git a/...ldb-ora/load-trgs/Bioentry_Rel_Assocs.trg → ...ldb-ora/load-trgs/Bioentry_Rel_Assocs.trg b/...ldb-ora/load-trgs/Bioentry_Rel_Assocs.trg → ...ldb-ora/load-trgs/Bioentry_Rel_Assocs.trg
diff --git a/...l/biosqldb-ora/load-trgs/Biosequences.trg → ...l/biosqldb-ora/load-trgs/Biosequences.trg b/...l/biosqldb-ora/load-trgs/Biosequences.trg → ...l/biosqldb-ora/load-trgs/Biosequences.trg
diff --git a/...biosqldb-ora/load-trgs/Chr_Map_Assocs.trg → ...biosqldb-ora/load-trgs/Chr_Map_Assocs.trg b/...biosqldb-ora/load-trgs/Chr_Map_Assocs.trg → ...biosqldb-ora/load-trgs/Chr_Map_Assocs.trg
diff --git a/...ql/biosqldb-ora/load-trgs/Chromosomes.trg → ...ql/biosqldb-ora/load-trgs/Chromosomes.trg b/...ql/biosqldb-ora/load-trgs/Chromosomes.trg → ...ql/biosqldb-ora/load-trgs/Chromosomes.trg
diff --git a/...l/sql/biosqldb-ora/load-trgs/Comments.trg → ...l/sql/biosqldb-ora/load-trgs/Comments.trg b/...l/sql/biosqldb-ora/load-trgs/Comments.trg → ...l/sql/biosqldb-ora/load-trgs/Comments.trg
diff --git a/...ql/biosqldb-ora/load-trgs/DB_Releases.trg → ...ql/biosqldb-ora/load-trgs/DB_Releases.trg b/...ql/biosqldb-ora/load-trgs/DB_Releases.trg → ...ql/biosqldb-ora/load-trgs/DB_Releases.trg
diff --git a/...a/load-trgs/Location_Qualifier_Assocs.trg → ...a/load-trgs/Location_Qualifier_Assocs.trg b/...a/load-trgs/Location_Qualifier_Assocs.trg → ...a/load-trgs/Location_Qualifier_Assocs.trg
diff --git a/...db-ora/load-trgs/Ontology_Term_Assocs.trg → ...db-ora/load-trgs/Ontology_Term_Assocs.trg b/...db-ora/load-trgs/Ontology_Term_Assocs.trg → ...db-ora/load-trgs/Ontology_Term_Assocs.trg
diff --git a/...biosqldb-ora/load-trgs/Ontology_Terms.trg → ...biosqldb-ora/load-trgs/Ontology_Terms.trg b/...biosqldb-ora/load-trgs/Ontology_Terms.trg → ...biosqldb-ora/load-trgs/Ontology_Terms.trg
diff --git a/...sql/biosqldb-ora/load-trgs/References.trg → ...sql/biosqldb-ora/load-trgs/References.trg b/...sql/biosqldb-ora/load-trgs/References.trg → ...sql/biosqldb-ora/load-trgs/References.trg
diff --git a/...sqldb-ora/load-trgs/Seqfeature_Assocs.trg → ...sqldb-ora/load-trgs/Seqfeature_Assocs.trg b/...sqldb-ora/load-trgs/Seqfeature_Assocs.trg → ...sqldb-ora/load-trgs/Seqfeature_Assocs.trg
diff --git a/...db-ora/load-trgs/Seqfeature_Locations.trg → ...db-ora/load-trgs/Seqfeature_Locations.trg b/...db-ora/load-trgs/Seqfeature_Locations.trg → ...db-ora/load-trgs/Seqfeature_Locations.trg
diff --git a/...load-trgs/Seqfeature_Qualifier_Assocs.trg → ...load-trgs/Seqfeature_Qualifier_Assocs.trg b/...load-trgs/Seqfeature_Qualifier_Assocs.trg → ...load-trgs/Seqfeature_Qualifier_Assocs.trg
diff --git a/...qldb-ora/load-trgs/Seqfeature_Sources.trg → ...qldb-ora/load-trgs/Seqfeature_Sources.trg b/...qldb-ora/load-trgs/Seqfeature_Sources.trg → ...qldb-ora/load-trgs/Seqfeature_Sources.trg
diff --git a/...ql/biosqldb-ora/load-trgs/Seqfeatures.trg → ...ql/biosqldb-ora/load-trgs/Seqfeatures.trg b/...ql/biosqldb-ora/load-trgs/Seqfeatures.trg → ...ql/biosqldb-ora/load-trgs/Seqfeatures.trg
diff --git a/...l/biosqldb-ora/load-trgs/Similarities.trg → ...l/biosqldb-ora/load-trgs/Similarities.trg b/...l/biosqldb-ora/load-trgs/Similarities.trg → ...l/biosqldb-ora/load-trgs/Similarities.trg
diff --git a/...ql/biosqldb-ora/load-trgs/Term_Assocs.trg → ...ql/biosqldb-ora/load-trgs/Term_Assocs.trg b/...ql/biosqldb-ora/load-trgs/Term_Assocs.trg → ...ql/biosqldb-ora/load-trgs/Term_Assocs.trg
diff --git a/...osql/sql/biosqldb-ora/load-trgs/Terms.trg → ...osql/sql/biosqldb-ora/load-trgs/Terms.trg b/...osql/sql/biosqldb-ora/load-trgs/Terms.trg → ...osql/sql/biosqldb-ora/load-trgs/Terms.trg
diff --git a/...db-ora/migrate/1.0/biosqldb-ora-1.0.1.sql → ...db-ora/migrate/1.0/biosqldb-ora-1.0.1.sql b/...db-ora/migrate/1.0/biosqldb-ora-1.0.1.sql → ...db-ora/migrate/1.0/biosqldb-ora-1.0.1.sql
diff --git a/.../biosqldb-ora/migrate/1.0/migrate-all.sql → .../biosqldb-ora/migrate/1.0/migrate-all.sql b/.../biosqldb-ora/migrate/1.0/migrate-all.sql → .../biosqldb-ora/migrate/1.0/migrate-all.sql
diff --git a/.../migrate/singapore/migrate-add-tables.sql → .../migrate/singapore/migrate-add-tables.sql b/.../migrate/singapore/migrate-add-tables.sql → .../migrate/singapore/migrate-add-tables.sql
diff --git a/...ra/migrate/singapore/migrate-bioentry.sql → ...ra/migrate/singapore/migrate-bioentry.sql b/...ra/migrate/singapore/migrate-bioentry.sql → ...ra/migrate/singapore/migrate-bioentry.sql
diff --git a/...ra/migrate/singapore/migrate-colnames.sql → ...ra/migrate/singapore/migrate-colnames.sql b/...ra/migrate/singapore/migrate-colnames.sql → ...ra/migrate/singapore/migrate-colnames.sql
diff --git a/...ra/migrate/singapore/migrate-ontology.sql → ...ra/migrate/singapore/migrate-ontology.sql b/...ra/migrate/singapore/migrate-ontology.sql → ...ra/migrate/singapore/migrate-ontology.sql
diff --git a/...db-ora/migrate/singapore/migrate-refs.sql → ...db-ora/migrate/singapore/migrate-refs.sql b/...db-ora/migrate/singapore/migrate-refs.sql → ...db-ora/migrate/singapore/migrate-refs.sql
diff --git a/...db-ora/migrate/singapore/migrate-rels.sql → ...db-ora/migrate/singapore/migrate-rels.sql b/...db-ora/migrate/singapore/migrate-rels.sql → ...db-ora/migrate/singapore/migrate-rels.sql
diff --git a/...b-ora/migrate/singapore/migrate-taxon.sql → ...b-ora/migrate/singapore/migrate-taxon.sql b/...b-ora/migrate/singapore/migrate-taxon.sql → ...b-ora/migrate/singapore/migrate-taxon.sql
diff --git a/...igrate/singapore/migrate-to-singapore.sql → ...igrate/singapore/migrate-to-singapore.sql b/...igrate/singapore/migrate-to-singapore.sql → ...igrate/singapore/migrate-to-singapore.sql
diff --git a/biosql/biosql/sql/biosqldb-pg.sql → Orthologs/biosql/biosql/sql/biosqldb-pg.sql b/biosql/biosql/sql/biosqldb-pg.sql → Orthologs/biosql/biosql/sql/biosqldb-pg.sql
diff --git a/biosql/biosql/sql/biosqldb-sqlite.sql → ...ogs/biosql/biosql/sql/biosqldb-sqlite.sql b/biosql/biosql/sql/biosqldb-sqlite.sql → ...ogs/biosql/biosql/sql/biosqldb-sqlite.sql
diff --git a/biosql/biosql/sql/biosqldb-views-pg.sql → ...s/biosql/biosql/sql/biosqldb-views-pg.sql b/biosql/biosql/sql/biosqldb-views-pg.sql → ...s/biosql/biosql/sql/biosqldb-views-pg.sql
diff --git a/biosql/biosql/sql/drop-biosqldb-hsqldb.sql → ...iosql/biosql/sql/drop-biosqldb-hsqldb.sql b/biosql/biosql/sql/drop-biosqldb-hsqldb.sql → ...iosql/biosql/sql/drop-biosqldb-hsqldb.sql
diff --git a/biosql/biosql/sql/drop-phylo.sql → Orthologs/biosql/biosql/sql/drop-phylo.sql b/biosql/biosql/sql/drop-phylo.sql → Orthologs/biosql/biosql/sql/drop-phylo.sql
diff --git a/biosql/biosql/sql/drop-phylodata.sql → ...logs/biosql/biosql/sql/drop-phylodata.sql b/biosql/biosql/sql/drop-phylodata.sql → ...logs/biosql/biosql/sql/drop-phylodata.sql
diff --git a/biosql/biosql/sql/drop-tables.sql → Orthologs/biosql/biosql/sql/drop-tables.sql b/biosql/biosql/sql/drop-tables.sql → Orthologs/biosql/biosql/sql/drop-tables.sql
diff --git a/...biosql/sql/migrate/biosql-mysql-1.0.1.sql → ...biosql/sql/migrate/biosql-mysql-1.0.1.sql b/...biosql/sql/migrate/biosql-mysql-1.0.1.sql → ...biosql/sql/migrate/biosql-mysql-1.0.1.sql
diff --git a/...ql/biosql/sql/migrate/biosql-pg-1.0.1.sql → ...ql/biosql/sql/migrate/biosql-pg-1.0.1.sql b/...ql/biosql/sql/migrate/biosql-pg-1.0.1.sql → ...ql/biosql/sql/migrate/biosql-pg-1.0.1.sql
diff --git a/biosql/biosql/sql/phylodb-topo-queries.sql → ...iosql/biosql/sql/phylodb-topo-queries.sql b/biosql/biosql/sql/phylodb-topo-queries.sql → ...iosql/biosql/sql/phylodb-topo-queries.sql
diff --git a/biosql/biosqldb-sqlite.sql → Orthologs/biosql/biosqldb-sqlite.sql b/biosql/biosqldb-sqlite.sql → Orthologs/biosql/biosqldb-sqlite.sql
diff --git a/biosql/load_ncbi_taxonomy.pl → Orthologs/biosql/load_ncbi_taxonomy.pl b/biosql/load_ncbi_taxonomy.pl → Orthologs/biosql/load_ncbi_taxonomy.pl
diff --git a/biosql/vall-biosqldb-sqlite.sql → Orthologs/biosql/vall-biosqldb-sqlite.sql b/biosql/vall-biosqldb-sqlite.sql → Orthologs/biosql/vall-biosqldb-sqlite.sql
diff --git a/Orthologs/blasting test.py b/Orthologs/blasting test.py
@@ -0,0 +1,7 @@
+from Orthologs.manager.blast.blastn import BLASTn
+
+x = BLASTn('MAFV3.2.csv')  # This is a template for GPCR project
+
+BLASTER = x.blast_config
+
+BLASTER(x.blast_human, 'Homo_sapiens', auto_start=True)
diff --git a/blast/README.md → Orthologs/genbank/README.md b/blast/README.md → Orthologs/genbank/README.md
diff --git a/genbank/db2fasta.py → Orthologs/genbank/db2fasta.py b/genbank/db2fasta.py → Orthologs/genbank/db2fasta.py
diff --git a/genbank/db2gbk.py → Orthologs/genbank/db2gbk.py b/genbank/db2gbk.py → Orthologs/genbank/db2gbk.py
diff --git a/genbank/gbk2fasta.py → Orthologs/genbank/gbk2fasta.py b/genbank/gbk2fasta.py → Orthologs/genbank/gbk2fasta.py
diff --git a/Orthologs/manager/README.md b/Orthologs/manager/README.md
@@ -0,0 +1,195 @@
+## Using Lister
+
+Lister is a class that creates a Lister object, which grants access to all of the initial data that we will use for the project.
+
+## Description
+
+The data to beinitialized includes the following:
+
+* Master_Accession_File.csv (include project name)
+* common_names.csv (PAML) (rename)
+* taxon_ids.txt
+
+ **Add some examples of these files as template**
+
+## Usage
+Using docstrings for help:
+```python
+>>> from manager.lister import Lister
+>>> help(Lister)
+```
+Using this class is simple:
+```python
+>>> from lister import Lister
+>>> from pprint import pprint
+>>> x = Lister(acc_file = 'Master_Accession_File.csv', paml_file = 'common_names.csv', taxon_file = 'taxon_ids.txt')
+```
+Lister uses pandas to manipulate our data so that we can more easily call it other processes.
+
+###Parameters
+```python
+from lister import Lister
+x = Lister(acc_file, paml_file, taxon_file, go_list = None, hgnc_file = False)
+```
+* **acc_file** (*'Master_Accession_file.csv'*) - Contains accession numbers for a group of genes ranked by tier.  Each gene has a group of
+orthlogs used in our phylogenetic anlysis.
+* **paml_file** (*'commonnames.csv'*) - Contains a list of shortened organism names used in the MSA files.  This is done to compy with
+PAML.
+* **taxon_file** (*'taxon_ids.txt'*) - Contains an ordered list of taxon ids
+* **go_list** (*[[gene.1, org.1], ... , [gene.n, org.n]]*) - A nested list that can be used to get information about specific gene/org pairs.
+* **hgnc_file** - For future implementation.  Used as a file handle to parse an HGNC *.csv* file.
+
+###Variables
+* x.gene_count
+* x.org_count
+* x.paml_org_list
+* x.taxon_ids
+
+###Lists
+List that contain header info(**x.header**):
+```python
+>>>pprint(x.header)
+['Tier',
+ 'Gene',
+ 'Homo_sapiens',
+ 'Macaca_mulatta',
+ 'Mus_musculus',
+ 'Rattus_norvegicus',
+...
+ 'Trichechus_manatus_latirostris',
+ 'Tupaia_chinensis',
+ 'Tursiops_truncatus']
+```
+List of Accessions (**x.acc_list**):
+```python
+>>> pprint(x.acc_list)
+['NM_000680.3',
+ 'NM_000679.3',
+ 'NM_000678.3',
+...
+ 'xm_004368425.2',
+ 'XM_006155397.2',
+ 'XM_004317686.1']
+```
+List of Genes (**x.gene_list**):
+```python
+>>> pprint(x.gene_list)
+['ADRA1A',
+ 'ADRA1B',
+ 'CHRM2',
+ ...
+ 'SSTR2',
+ 'TSHR',
+ 'VIPR1']
+```
+List of Organisms (**x.org_list**):
+```python
+>>> pprint(x.org_list)
+['Homo_sapiens',
+ 'Macaca_mulatta',
+ 'Mus_musculus',
+ 'Rattus_norveg',
+...
+'Trichechus_manatus_latirostris',
+ 'Tupaia_chinensis',
+ 'Tursiops_truncatus']
+```
+###Dictionaries
+Dictionary of Accessions is a nested list(**x.acc_dict**):
+```python
+>>> pprint(x.acc_dict)
+{'NM_000115.3': ['EDNRB', 'Homo_sapiens'],
+ 'NM_000145.3': ['FSHR', 'Homo_sapiens'],
+ 'NM_000164.3': ['GIPR', 'Homo_sapiens'],
+...
+ 'NM_001001620.1': ['CCR3', 'Sus_scrofa'],
+ 'NM_001002911.3': ['GPR139', 'Homo_sapiens'],
+ 'NM_001002944.1': ['ADORA2B', 'Canis_lupus_familiaris']}
+```
+Dictionary of Genes is a nested dictionary. (**x.gene_dict**, **x.tier_dict**):
+```python
+>>> pprint(x.gene_dict['HTR1A'])
+{'Ailuropoda_melanoleuca': 'XM_002926305.1',
+ 'Bos_taurus': 'XM_600535.5',
+ 'Callithrix_jacchus': 'XM_008992005.2',
+ ...
+ 'Tier': '1',
+ 'Trichechus_manatus_latirostris': 'xm_004374552.2',
+ 'Tupaia_chinensis': 'xm_006156821.1',
+ 'Tursiops_truncatus': 'xm_004325159.1'}
+###########################################################################
+>>> pprint(x.tier_dict['HTR1A'])
+'1'
+```
+Dictionary of Organisms is a nested dictionary (**x.org_dict**)
+```python
+>>> HS_query = x.org_dict['Homo_sapiens'].values()
+>>> HS_gene_list = x.org_dict['Homo_sapiens'].keys()
+>>> pprint(list(HS_query))
+['NM_000680.3',
+ 'NM_000679.3',
+ 'NM_000678.3',
+...
+ 'XM_011517263.2',
+ 'NM_000369.2',
+ 'NM_004624.3']
+```
+Dictionar
+
+###Dataframes
+Dataframe that uses Gene as an index(**x.df**):
+```python
+>>> pprint(x.df.T.HTR1A)
+Tier                                            1
+Homo_sapiens                          NM_000524.3
+Macaca_mulatta                     NM_001198700.1
+Mus_musculus                          NM_008308.4
+...
+Tupaia_chinensis                   xm_006156821.1
+Tursiops_truncatus                 xm_004325159.1
+Name: HTR1A, dtype: object
+```
+Pivot Table MultiIndexed with pandas(**x.pt**):
+```python
+# #### Format the main pivot table #### #
+self.pt = pd.pivot_table(pd.read_csv(self.__filename_path), index=['Tier', 'Gene'], aggfunc='first')
+array = self.pt.axes[1].tolist() # Organism list
+self.pt.columns = pd.Index(array, name='Organism')
+```
+
+Dictionary of Dataframes that correspond to tiers (**x.get_tier_frame**, **x.tier_frame_dict**):
+```python
+>>> Tiers = x.get_tier_frame('1')
+>>> Tiers.keys()
+dict_keys(['1'])
+>>> Tiers = x.tier_frame_dict()
+>>> Tiers.keys()
+dict_keys(['1', '2', '3', 'None'])
+```
+
+###Methods
+Lookup Accessions (**x.get_accession(gene, org)**, **x.get_accesions(go_list=None)**)
+```python
+>>> x.get_accession('HTR1A', 'Homo_sapiens')
+'NM_000524.3'
+>>> go_list = [['HTR1A', 'Homo_sapiens'], ['HTR1A', 'Macaca_mulatta']]
+>>> x.get_accessions(go_list = go_list)
+['NM_000524.3', 'NM_001198700.1']
+```
+Lookup a list of Accession for alignment(**x.get_accession_alignment(gene)**):
+```python
+>>> pprint(x.get_accession_alignment('HTR1A'))
+['NM_000524.3',
+ 'NM_001198700.1',
+...
+ 'xm_006156821.1',
+ 'xm_004325159.1']
+```
+Get the master lists from a new dataframe(**self.get_master_list(df)**):
+```python
+>>> from manager.lister import Lister
+>>> import os
+>>> from pathlib import Path
+>>> y = Lister()
+>>> y.get_master_lists(csv_file='MAFV3.1.csv')
+```